Combined inhibition of the vitamin d receptor and poly(adp) ribose polymerase (parp) in the treatment of cancer

ABSTRACT

Methods for treating tumors comprise contacting tumor cells expressing the vitamin D receptor with a vitamin D receptor ligand that inhibits homologous recombination in the tumor cells, and contacting the tumor cells with an amount of a Poly(ADP) Ribose Polymerase 1 (PARP-1) inhibitor. Inhibiting homologous recombination produces a synergistic therapeutic effect between the vitamin D receptor ligand and PARP-1 inhibitor, and may overcome PARP-1 resistance in killing tumor cells.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.62/063,581, filed on Oct. 14, 2014, the contents of which areincorporated by reference herein, in their entirety and for allpurposes.

STATEMENT OF GOVERNMENT SUPPORT

The inventions described herein were made, in part, with funds obtainedfrom the National Institutes of Health, Grant No. CA 169706. The U.S.government may have certain rights in these inventions.

REFERENCE TO A SEQUENCE LISTING

This application includes a Sequence Listing submitted electronically asa text file named VDR+PARP_ST25.txt, created on Oct. 9, 2015, with asize of 3000 bytes. The Sequence Listing is incorporated by referenceherein.

FIELD OF THE INVENTION

The invention relates generally to the field of cancer treatment. Moreparticularly, the invention relates to combination therapies fortreating cancer cells expressing the vitamin D receptor, especiallypancreatic cancer cells, by inhibiting homologous recombination in suchcells, thereby enhancing the susceptibility of the cells to inhibitorsof poly(ADP)-ribose polymerase (PARP).

BACKGROUND OF THE INVENTION

Various publications, including patents, published applications,technical articles and scholarly articles are cited throughout thespecification. Each of these cited publications is incorporated byreference herein, in its entirety and for all purposes.

Pancreatic cancer (PCa) is the 4th leading cause of cancer fatality inthe United States and has the lowest 5-year survival rate of any majorcancer (ACS). More than 70% of patients die within the first year afterbeing diagnosed. By year 2020, it is anticipated that PCa will move tothe 2nd leading cause of cancer death. At the time of diagnosis, over52% of the patients have distant disease and 26% have regional spread.Only ˜15% of patients diagnosed with pancreatic adenocarcinoma can havetheir tumors surgically removed. Lack of early diagnosis, complexbiology of the disease, and limited treatment options contribute tomaking PCa a major killer.

Virtually all pancreatic tumors are adenocarcinomas of which the vastmajority expresses a mutant K-Ras. Over two decades of PCa researchsuggest a model for disease progression where early, low-gradepancreatic intraepithelial neoplasia (PanIN), is associated with KRAS2mutations and telomere shortening. Intermediate and late stages of thedisease are characterized by loss of p16/CDKN2A, SMAD4, p53, and BRCA2respectively. Additionally, a massive effort to sequence the genomes of24 independently derived advanced pancreatic adenocarcinomas revealed aremarkably complex pattern of genetic mutations. On average, there were63 genetic mutations in PCa. The majority (67%) of the mutations couldbe classified into 12 partially overlapping cellular signaling pathways.

PCas are notoriously insensitive to the backbone of cancer chemo- andradiation therapy, all of which target processes essential for theintegrity of the genome. Understanding the mechanisms of chemoresistanceof PCa will provide new targets that enhance cell killing.

SUMMARY OF THE INVENTION

The disclosure features combination therapies for treating cancer cellsexpressing the vitamin D receptor (VDR), and especially its use forenhancing the susceptibility of cancer cells to Poly(ADP) RibosePolymerase 1 (PARP-1) inhibition, for example, by inactivating thisreceptor in order to inhibit homologous recombination in the cells. Itis believed that the efficacy of PARP inhibition hinges, at least inpart, on impaired or a lack of homologous recombination.

In some aspects, the therapeutic methods comprise killing tumor cellsexpressing the vitamin D receptor by contacting the vitamin D receptoron the tumor cells with a vitamin D receptor ligand, and contacting thetumor cells with an amount of a Poly(ADP) Ribose Polymerase 1 (PARP-1)inhibitor. The combination of the vitamin D receptor ligand and PARP-1inhibitor exhibits therapeutic synergy in killing the tumor cells. Theligand may inactivate vitamin D receptor-mediated homologousrecombination. The tumor cells may be resistant to the PARP-1 inhibitor.The tumor cells may be pancreatic tumor cells, lung tumor cells, breasttumor cells, ovarian tumor cells, lymph node tumor cells, bladder tumorcells, prostate tumor cells, or esophageal tumor cells. Pancreatic tumorcells are preferred. The method is preferably carried out in vivo, andmore preferably in a human subject.

The vitamin D receptor ligand may be an agonist or antagonist of thevitamin D receptor, or may competitively inhibit a second ligand that isexpressed by the tumor, with this second ligand having some activitythat induces, enhances, facilitates, potentiates, or otherwise causesvitamin D Receptor activity that protects the tumor, for example, viahomologous recombination and DNA repair. The ligand may be used in anamount effective to inhibit homologous recombination in the tumor cells.The ligand may be a vitamin D analog. The vitamin D receptor ligand maybe an antagonist of the vitamin D receptor. The ligand may comprisecalcitriol, calcipotriol, eldecalcitol, lisinopril, elocalcitol,paricalcitol, seocalcitol, or any combination thereof. The ligand maycomprise TEI-9647, TEI-9648, OU-72 (U.S. Publ. No. 2005/0182033), or aderivative or analog thereof. The PARP-1 inhibitor may compriseolaparib, iniparib, rucaparib, veliparib, MK 4827, BMN673, BSI 401, orany combination thereof.

Alternatively to contacting the vitamin D receptor with a ligand, themethod may comprise inhibiting the expression of the vitamin D receptor,for example, by transforming the tumor cells with a nucleic acidmolecule that inhibits the expression of the vitamin D receptor in thetumor cells. The combination of inhibiting the expression of the vitaminD receptor and PARP-1 inhibition exhibits therapeutic synergy in killingthe tumor cells.

The method may further comprise inducing double stranded DNA breaks inthe chromosomal DNA of the tumor cells. Inducing double stranded DNAbreaks may comprise irradiating the chromosomal DNA of the tumor cells.Inducing double stranded DNA breaks may comprise contacting the tumorcells with an amount of gemcitabine effective to induce double strandedDNA breaks.

In some detailed aspects, the method comprises contacting the vitamin Dreceptor of the pancreatic tumor cells with a vitamin D receptor ligand,and then contacting the pancreatic tumor cells with an amount of thePARP-1 inhibitor. The combination the vitamin D receptor ligand andPARP-1 inhibitor exhibits therapeutic synergy in killing the pancreatictumor cells. The pancreatic tumor cells may be resistant to the PARP-1inhibitor. The vitamin D receptor ligand may be an agonist or antagonistof the vitamin D receptor, or may competitively inhibit a second ligandthat is expressed by the tumor, with this second ligand having someactivity that induces, enhances, facilitates, potentiates, or otherwisecauses vitamin D Receptor activity that protects the tumor, for example,via homologous recombination and DNA repair. The ligand may be used inan amount effective to inhibit homologous recombination in the tumorcells. The ligand may be a vitamin D analog. The vitamin D receptorligand may be an antagonist of the vitamin D receptor. The ligand maycomprise calcitriol, calcipotriol, eldecalcitol, lisinopril,elocalcitol, paricalcitol, seocalcitol, or any combination thereof. Theligand may comprise TEI-9647, TEI-9648, OU-72, or a derivative or analogthereof. The PARP-1 inhibitor may comprise olaparib, iniparib,rucaparib, veliparib, MK 4827, BMN673, BSI 401, or any combinationthereof. The method may further comprise inducing double stranded DNAbreaks in the chromosomal DNA of the tumor cells. Inducing doublestranded DNA breaks may comprise irradiating the chromosomal DNA of thetumor cells. Inducing double stranded DNA breaks may comprise contactingthe tumor cells with an amount of gemcitabine effective to induce doublestranded DNA breaks.

In some aspects, the therapeutic methods comprise killing tumor cells byinhibiting Rad51 in the tumor cells sufficiently to inhibit homologousrecombination in the tumor cells, and contacting the tumor cells with anamount of a Poly(ADP) Ribose Polymerase 1 (PARP-1) inhibitor. Thecombination of Rad51 inhibition and PARP-1 inhibition exhibitstherapeutic synergy in killing the tumor cells. The tumor cells may beresistant to the PARP-1 inhibitor. The tumor cells may be pancreatictumor cells, lung tumor cells, breast tumor cells, ovarian tumor cells,lymph node tumor cells, bladder tumor cells, prostate tumor cells, oresophageal tumor cells. Pancreatic tumor cells are preferred. The methodis preferably carried out in vivo, and more preferably in a humansubject.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Sensitization of pancreatic cancer cells to gemcitabinefollowing VDR knockdown. (A) Colony formation assay comparinggemcitabine sensitivity of Panc1 cells after control, VDR and Chk1 siRNAtransfection. Cells were treated with 50 nM gemcitabine for 24 hrs. anddrug removed before the assay. Colony counts are presented beneath theimage of a representative colony survival assay. (B) Gemcitabine killcurves from clonogenic survival assays performed on BXPC3, Panc1 andCFPAC1 cells following control or VDR siRNA transfection (n=5). pvalues: BxPC3=0.036, Panc1=0.171, CFPAC1=0.083. (C) clonogenic survivalassays of gemcitabine sensitivity of BxPC3 VDRkd cells transfected withthe indicated VDR constructs (n=5). p values: VDR-WT=0.088,VDR-C288G=0.671, VDR-K246G=0.845, VDR-L254G=0.148. (D) AML1/ETO andVDR-S237M neutralizes the ability of WT-VDR to rescue gemcitabineresistance of BxPC3 VDRkd cells (n=5). p values: AML1/ETO=0.147,VDR-S237M=0.039. (E) Western blot showing VDR expression after 18 hourvehicle or gemcitabine (50 nM) treatment of PCa cell lines. 40 μg ofprotein loaded. Lane 1=Panc1+Vehicle; Lane 2=Panc1+gemcitabine; Lane3=CFPAC1+Vehicle; Lane 4=CFPAC1+gemcitabine; Lane 5=BxPC3+Vehicle; Lane6=BxPC3+gemcitabine. The 55 kDa marker is labeled between lanes 2 and 3,and to the right of lane 6. (F) Increased resistance of Panc1 cells togemcitabine following VDR 898 overexpression (n=5). p value=0.008.

FIG. 2: Gemcitabine sensitization after VDR knockdown is not due tooverride of the DNA damage checkpoint. Select frames from a 48 hrtimelapse of Panc1 cells transfected with control, Chk1, and VDR siRNAsthat were treated with vehicle or gemcitabine. Chk1 siRNA of gemcitabinetreated samples show increased mitotic cells at later timepoints.Enlarged images show brightfield and gfpH2B images of Chk1 siRNA cellsprematurely entering mitosis and undergoing mitotic catastrophe. VDRsiRNA transfected cells remain in interphase and die without everentering mitosis.

FIG. 3: VDR knockdown reduces gemcitabine induced γH2AX and Rad51 fociformation in BXPC3 and Panc1 cells. (A) Cells were treated with 50 nMgemcitabine, fixed at 0, 2 hrs, 3 hrs, 4 hrs, 6 hrs, 8 hrs, and 18 hrsand stained for Rad51, γH2AX, and 53BP1. Representative images (40×)from 0, 4, 8 and 18 hrs post drug treatments are shown. (B) Highermagnification (90×) confocal images of individual nuclei displaying thedifferent staining patterns of Rad51, γH2AX, and 53BP1 after VDRknockdown compared to controls. Percentages of each pattern from 500cells/sample analyzed are presented.

FIG. 4: Quantification of Rad51, γH2AX, and 53BP1 staining of BxPC3cells. Individual nuclei from images in FIG. 3 were separately analyzedfor foci number and focal intensity. Quantitation was performed on cellstreated with gemcitabine for 0, 2 hrs, 3 hrs, 4 hrs, 6 hrs, 8 hrs, and18 hrs. 500 cells from each timepoint was examined for Rad51, γH2AX, and53BP1.

FIG. 5: Quantification of Rad51, γH2AX, and 53BP1 staining of Panc 1cells. Individual nuclei from images in FIG. 3 were separately analyzedfor foci number and focal intensity. Quantitation was performed on cellstreated with gemcitabine for 0, 2 hrs, 3 hrs, 4 hrs, 6 hrs, 8 hrs, and18 hrs. 500 cells from each timepoint was examined for Rad51, γH2AX, and53BP1.

FIG. 6: VDR knockdown sensitizes BXPC3 and Panc1 cells to the PARPinhibitor, Rucaparib. blocks gemcitabine induced DSB HR repair byreducing Rad51 foci formation at DSBs. (A) Rucaparib kill curvesgenerated from clonogenic assays of cells transfected with control,BRCA1 and VDR siRNAs. (B) Western blot comparing Rad51 and γH2AX proteinlevels of BxPC3 and BxPC3 VDRkd cells. 40 μg of protein loaded. Lane1=BxPC3+vehicle (18 hrs) (supernatant fraction); Lane2=BxPC3+gemcitabine (50 nM) (18 hrs) (supernatant fraction); Lane3=BxPC3 VDRkd+vehicle (18 hrs) (supernatant fraction); Lane 4=BxPC3VDRkd+gemcitabine (50 nM) (18 hrs) (supernatant fraction); Lane5=BxPC3+vehicle (18 hrs) (pellet fraction); Lane 6=BxPC3+gemcitabine (50nM) (18 hrs) (pellet fraction); Lane 7=BxPC3 VDRkd+vehicle (18 hrs)(pellet fraction); Lane 8=BxPC3 VDRkd+gemcitabine (50 nM) (18 hrs)(pellet fraction). (C) Comparison of Rad51 and γH2AX staining of BxPC3and BxPC3kd cells following TSA (500 nM)+gemcitabine (50 nM) treatments.(D) Colony survival of BxPC3 VDRkd and BxPC3 parental cells treated withTSA (500 nM)+gemcitabine (n=3). P values: BxPC3 VDRkd=0.289, BxPC3control=0.02.

FIG. 7: p300 knockdown reduces gemcitabine induced Rad51 foci formation.(A) Rad51 and γH2AX staining of BxPC3 or Panc1 cells treated withcontrol and p300 shRNA's, and treated with vehicle or gemcitabine. (B)Clonogenic survival assay of BxPC3 and Panc1 cells transfected with p300shRNA and treated with different doses of gemcitabine (n=3). p values:BxPC3=0.0489, Panc1=0.192.

DETAILED DESCRIPTION OF THE INVENTION

Various terms relating to aspects of the present invention are usedthroughout the specification and claims. Such terms are to be giventheir ordinary meaning in the art, unless otherwise indicated. Otherspecifically defined terms are to be construed in a manner consistentwith the definition provided herein.

As used herein, the singular forms “a,” “an,” and “the” include pluralreferents unless expressly stated otherwise.

Knockdown includes the reduced expression of a gene. A knockdowntypically has at least about a 20% reduction in expression, preferablyhas at least about a 50% reduction in expression, and more preferablyhas at least about a 75% reduction in expression, and in some aspectshas at least about an 80% to about an 85% reduction in expression, atleast about an 85% to about a 90% reduction in expression, or about an80% to about a 90% reduction in expression, and in some aspects has agreater than 90% reduction in expression, or a greater than 95%reduction in expression.

Nucleic acid molecules include any chain of at least two nucleotides,which may be unmodified or modified RNA or DNA, hybrids of RNA and DNA,and may be single, double, or triple stranded.

Expression of a nucleic acid molecule includes the biosynthesis of agene product, including but not limited to the transcription of a geneinto RNA, the translation of RNA into a protein or polypeptide, and allnaturally occurring post-transcriptional and post-translationalmodifications thereof.

Inhibiting includes interfering with, reducing, decreasing, blocking,preventing, delaying, inactivating, antagonizing, desensitizing,stopping, knocking down (e.g., knockdown), and/or downregulating thebiologic activity or expression of a molecule, such as the vitamin Dreceptor, or pathway of interest, such as a signal pathway induced orpotentiated by vitamin D receptor activation.

It has been observed in accordance with the invention that knockdown ofvitamin D receptor (VDR) expression, or chemical inactivation of thisreceptor in cancer cells enhances sensitization of the cells toinhibition of PARP-1, with the result of synergistically-enhancedtumoricidal activity observed in tumor cells treated with thiscombination therapy, relative to tumor cells treated with either VDRinhibition or PARP-1 inhibition by itself. It has been further observedthat the VDR plays a role in homologous recombination. Homologousrecombination plays a role in the repair of double stranded DNA breaks.Thus, inhibition of homologous recombination-based double stranded DNAbreak repair via the VDR makes cancer cells more susceptible to PARPinhibition therapy, in line with the observation that the efficacy ofPARP inhibitors depends on cells having a diminished or no capacity tocarry out homologous recombination. Of note, inactivating the VDR runscontrary to the conventional understanding in the cancer treatment artbecause it has been established that vitamin D has antiproliferativeproperties such that the vitamin D receptor itself plays a positive rolein cancer treatment. Under the conventional understanding, any knockdownor inhibition of the vitamin D receptor would be expected to have adeleterious effect on cancer therapy. Accordingly, the inventionfeatures methods for treating tumors comprising cells expressing thevitamin D receptor. The methods may be carried out in vivo, ex vivo, invitro, or in situ.

In some aspects, a method for treating a tumor comprises contactingtumor cells with an effective amount of a vitamin D receptor ligand andcontacting the cells with an effective amount of an inhibitor or PARP-1.The combination of the VDR ligand and PARP-1 inhibitor produces atherapeutic synergy in killing the tumor cells relative the killing ofthe tumor cells induced by either the ligand or the PARP-1 inhibitoralone. Cell death may be enhanced in tumors resistant to PARP-1inhibitor therapy.

In some aspects, a method for treating a tumor comprises inhibiting theexpression of a constituent of the vitamin D receptor signaling pathwayin the cells and contacting the cells with an effective amount of aPARP-1 inhibitor. The constituent may be one or more of retinoidreceptor X (RXR), runt related transcription factor 2 (RUNX2), and zincfinger and BTB domain containing 16 (ZBT16). This latter gene is amember of the Krueppel C2H2-type zinc-finger protein family and encodesa zinc finger transcription factor that contains nine Kruppel-type zincfinger domains at the carboxyl terminus. In preferred aspects,inhibiting the expression of the constituent of the vitamin D receptorsignaling pathway in the cells enhances the level of PARPinhibitor-induced cell death in the tumor relative to the level of celldeath in a tumor of the same type contacted with the PARP inhibitor inwhich the expression of the constituent was not inhibited.

In any of the methods, the expression of the vitamin D receptor or aconstituent of the vitamin D receptor signaling pathway can beinhibited, for example, by transfecting tumor cells with a nucleic acidmolecule that interferes with the expression of the gene encoding thevitamin D receptor or a nucleic acid molecule that interferes with theexpression of the gene encoding the constituent of the vitamin Dreceptor signaling pathway such as RXR, RUNX2, and ZBTB16. Geneexpression can be inhibited, for example, through the use of a varietyof post-transcriptional gene silencing (RNA silencing) techniques.

RNA interference (RNAi) is a mechanism of post-transcriptional genesilencing mediated by double-stranded RNA (dsRNA), which is distinctfrom antisense and ribozyme-based approaches. RNA interference may beeffectuated, for example, by administering a nucleic acid (e.g., dsRNA)that hybridizes under stringent conditions to the gene encoding thevitamin D receptor, thereby attenuating its expression. RNA interferenceprovides shRNA or siRNA that comprise multiple sequences that target oneor more regions of the target gene. dsRNA molecules (shRNA or siRNA) arebelieved to direct sequence-specific degradation of mRNA in cells ofvarious types after first undergoing processing by an RNase III-likeenzyme called DICER into smaller dsRNA molecules comprised of two 21nucleotide (nt) strands, each of which has a 5′ phosphate group and a 3′hydroxyl, and includes a 19 nt region precisely complementary with theother strand, so that there is a 19 nt duplex region flanked by 2 nt-3′overhangs. RNAi is thus mediated by short interfering RNAs (siRNA),which typically comprise a double-stranded region approximately 19nucleotides in length with 1-2 nucleotide 3′ overhangs on each strand,resulting in a total length of between approximately 21 and 23nucleotides. In mammalian cells, dsRNA longer than approximately 30nucleotides typically induces nonspecific mRNA degradation via theinterferon response. However, the presence of siRNA in mammalian cells,rather than inducing the interferon response, results insequence-specific gene silencing.

Viral vectors or DNA vectors encode short hairpin RNA (shRNA) which areprocessed in the cell cytoplasm to short interfering RNA (siRNA). Ingeneral, a short, interfering RNA (siRNA) comprises an RNA duplex thatis preferably approximately 19 basepairs long and optionally furthercomprises one or two single-stranded overhangs or loops. A siRNA maycomprise two RNA strands hybridized together, or may alternativelycomprise a single RNA strand that includes a self-hybridizing portion.siRNAs may include one or more free strand ends, which may includephosphate and/or hydroxyl groups. siRNAs typically include a portionthat hybridizes under stringent conditions with a target transcript. Onestrand of the siRNA (or, the self-hybridizing portion of the siRNA) istypically precisely complementary with a region of the target transcript(e.g., vitamin D receptor transcript), meaning that the siRNA hybridizesto the target transcript without a single mismatch. In aspects in whichperfect complementarity is not achieved, it is generally preferred thatany mismatches be located at or near the siRNA termini.

siRNAs have been shown to downregulate gene expression when transferredinto mammalian cells by such methods as transfection, electroporation,cationic liposome-mediated transfection, or microinjection, or whenexpressed in cells via any of a variety of plasmid-based approaches. ThesiRNA may comprise two individual nucleic acid strands or of a singlestrand with a self-complementary region capable of forming a hairpin(stem-loop) structure. A number of variations in structure, length,number of mismatches, size of loop, identity of nucleotides inoverhangs, etc., are consistent with effective siRNA-triggered genesilencing. While not wishing to be bound by any theory, it is believedthat intracellular processing (e.g., by DICER) of a variety of differentprecursors results in production of siRNA capable of effectivelymediating gene silencing. Generally, it is preferred to target exonsrather than introns, and it may also be preferable to select sequencescomplementary to regions within the 3′ portion of the target transcript.Generally it is preferred to select sequences that contain anapproximately equimolar ratio of the different nucleotides and to avoidstretches in which a single residue is repeated multiple times.

siRNAs may thus comprise RNA molecules having a double-stranded regionapproximately 19 nucleotides in length with 1-2 nucleotide 3′ overhangson each strand, resulting in a total length of between approximately 21and 23 nucleotides. siRNAs also include various RNA structures that maybe processed in vivo to generate such molecules. Such structures includeRNA strands containing two complementary elements that hybridize to oneanother to form a stem, a loop, and optionally an overhang, preferably a3′ overhang. Preferably, the stem is approximately 19 bp long, the loopis about 1-20, more preferably about 4-10, and most preferably about 6-8nt long and/or the overhang is about 1-20, and more preferably about2-15 nt long. In certain aspects, the stem is minimally 19 nucleotidesin length and may be up to approximately 29 nucleotides in length. Loopsof 4 nucleotides or greater are less likely subject to stericconstraints than are shorter loops and therefore may be preferred. Theoverhang may include a 5′ phosphate and a 3′ hydroxyl. The overhang may,but need not comprise a plurality of U residues, e.g., between 1 and 5 Uresidues. Classical siRNAs as described above trigger degradation ofmRNAs to which they are targeted, thereby also reducing the rate ofprotein synthesis. In addition to siRNAs that act via the classicalpathway, certain siRNAs that bind to the 3′ UTR of a template transcriptmay inhibit expression of a protein encoded by the template transcriptby a mechanism related to but distinct from classic RNA interference,e.g., by reducing translation of the transcript rather than decreasingits stability. Such RNAs are referred to as microRNAs (miRNAs) and aretypically between approximately 20 and 26 nucleotides in length, e.g.,22 nt in length. It is believed that they are derived from largerprecursors known as small temporal RNAs (stRNAs) or mRNA precursors,which are typically approximately 70 nt long with an approximately 4-15nt loop. Endogenous RNAs of this type have been identified in a numberof organisms including mammals, suggesting that this mechanism ofpost-transcriptional gene silencing may be widespread. MicroRNAs havebeen shown to block translation of target transcripts containing targetsites.

siRNAs such as naturally occurring or artificial (i.e., designed byhumans) mRNAs that bind within the 3′ UTR (or elsewhere in a targettranscript) and inhibit translation may tolerate a larger number ofmismatches in the siRNA/template duplex, and particularly may toleratemismatches within the central region of the duplex. In fact, there isevidence that some mismatches may be desirable or required as naturallyoccurring stRNAs frequently exhibit such mismatches as do mRNAs thathave been shown to inhibit translation in vitro. For example, whenhybridized with the target transcript such siRNAs frequently include twostretches of perfect complementarity separated by a region of mismatch.A variety of structures are possible. For example, the mRNA may includemultiple areas of nonidentity (mismatch). The areas of nonidentity(mismatch) need not be symmetrical in the sense that both the target(e.g., the vitamin D receptor, vitamin D receptor signal pathwayconstituent, or mutant p53) and the mRNA include nonpaired nucleotides.Typically the stretches of perfect complementarity are at least 5nucleotides in length, e.g., 6, 7, or more nucleotides in length, whilethe regions of mismatch may be, for example, 1, 2, 3, or 4 nucleotidesin length.

Hairpin structures designed to mimic siRNAs and mRNA precursors areprocessed intracellularly into molecules capable of reducing orinhibiting expression of target transcripts (e.g., the vitamin Dreceptor, vitamin D receptor signal pathway constituent, or mutant p53).These hairpin structures, which are based on classical siRNAs consistingof two RNA strands forming a 19 bp duplex structure are classified asclass I or class II hairpins. Class I hairpins incorporate a loop at the5′ or 3′ end of the antisense siRNA strand (i.e., the strandcomplementary to the target transcript whose inhibition is desired) butare otherwise identical to classical siRNAs. Class II hairpins resemblemRNA precursors in that they include a 19 nt duplex region and a loop ateither the 3′ or 5′ end of the antisense strand of the duplex inaddition to one or more nucleotide mismatches in the stem. Thesemolecules are processed intracellularly into small RNA duplex structurescapable of mediating silencing. They appear to exert their effectsthrough degradation of the target mRNA rather than through translationalrepression as is thought to be the case for naturally occurring mRNAsand stRNAs.

Thus, a diverse set of RNA molecules containing duplex structures isable to mediate silencing through various mechanisms. Any such RNA, oneportion of which binds to a target transcript (e.g., the vitamin Dreceptor, vitamin D receptor signal pathway constituent, or mutant p53)and reduces its expression, whether by triggering degradation, byinhibiting translation, or by other means, may be considered an siRNA,and any structure that generates such an siRNA (i.e., serves as aprecursor to the RNA) is useful.

A further method of RNA interference is the use of short hairpin RNAs(shRNA). A plasmid containing a DNA sequence encoding for a particulardesired siRNA sequence is delivered into a target cell via transfectionor virally-mediated infection. Once in the cell, the DNA sequence iscontinuously transcribed into RNA molecules that loop back on themselvesand form hairpin structures through intramolecular base pairing. Thesehairpin structures, once processed by the cell, are equivalent totransfected siRNA molecules and are used by the cell to mediate RNAi ofthe desired protein. The use of shRNA has an advantage over siRNAtransfection as the former can lead to stable, long-term inhibition ofprotein expression. Inhibition of protein expression by transfectedsiRNAs is a transient phenomenon that does not occur for times periodslonger than several days. In some cases, though, this may be preferableand desired. In cases where longer periods of protein inhibition arenecessary, shRNA mediated inhibition is preferable. The use of shRNA ispreferred for some aspects of the invention. Typically, siRNA-encodingvectors are constructs comprising a promoter, a sequence of the targetgene to be silenced in the sense orientation, a spacer, the antisense ofthe target gene sequence, and a terminator.

Inhibition of the expression of the vitamin D receptor, a vitamin Dreceptor signal pathway constituent, or mutant p53 can also beeffectuated by other means that are known and readily practiced in theart. For example, antisense nucleic acids can be used. Antisense RNAtranscripts have a base sequence complementary to part or all of anyother RNA transcript in the same cell. Such transcripts modulate geneexpression through a variety of mechanisms including the modulation ofRNA splicing, the modulation of RNA transport and the modulation of thetranslation of mRNA. Accordingly, in certain aspects, inhibition of theexpression of the vitamin D receptor in a cell can be accomplished byexpressing an antisense nucleic acid molecule in the cell.

Antisense nucleic acids are generally single-stranded nucleic acids(DNA, RNA, modified DNA, or modified RNA) complementary to a portion ofa target nucleic acid (e.g., an mRNA transcript) and therefore able tobind to the target to form a duplex. Typically, they areoligonucleotides that range from 15 to 35 nucleotides in length but mayrange from 10 up to approximately 50 nucleotides in length. Bindingtypically reduces or inhibits the expression of the target nucleic acid,such as the gene encoding the target signal protein. For example,antisense oligonucleotides may block transcription when bound to genomicDNA, inhibit translation when bound to mRNA, and/or lead to degradationof the nucleic acid. Inhibition of the expression of the vitamin Dreceptor, a vitamin D receptor signal pathway constituent, or mutant p53can be achieved by the administration of antisense nucleic acidscomprising sequences complementary to those of the mRNA that encodes thevitamin D receptor, the vitamin D receptor signal pathway constituent,or mutant p53.

Antisense oligonucleotides can be synthesized with a base sequence thatis complementary to a portion of any RNA transcript in the cell.Antisense oligonucleotides can modulate gene expression through avariety of mechanisms including the modulation of RNA splicing, themodulation of RNA transport and the modulation of the translation ofmRNA. Various properties of antisense oligonucleotides includingstability, toxicity, tissue distribution, and cellular uptake andbinding affinity may be altered through chemical modifications including(i) replacement of the phosphodiester backbone (e.g., peptide nucleicacid, phosphorothioate oligonucleotides, and phosphoramidateoligonucleotides), (ii) modification of the sugar base (e.g.,2′-O-propylribose and 2′-methoxyethoxyribose), and (iii) modification ofthe nucleoside (e.g., C-5 propynyl U, C-5 thiazole U, and phenoxazineC).

Inhibition of the vitamin D receptor or vitamin D receptor signalpathway constituent can also be effectuated by use of ribozymes. Certainnucleic acid molecules referred to as ribozymes or deoxyribozymes havebeen shown to catalyze the sequence-specific cleavage of RNA molecules.The cleavage site is determined by complementary pairing of nucleotidesin the RNA or DNA enzyme with nucleotides in the target RNA. Thus, RNAand DNA enzymes can be designed to cleave to any RNA molecule, therebyincreasing its rate of degradation.

Gene expression may also be accomplished using CRISPR/Cas9 targetedgenome editing. This uses a short RNA that is complementary to the geneof interest, for example, the VDR gene. The cas9 nuclease recognizes theregion of complementarity, cuts the DNA (the genomic locus) anderror-prone repair will introduce frameshift mutations that effectivelyinactivate the gene. This introduces a permanent mutation at the genomiclevel, and is thus permanent-as opposed to the other technologies thatwane overtime because the mRNA is constantly being made.

In some aspects, the cells can be specifically transformed withtranscription-silencing nucleic acids such as shRNA or siRNA, or can betransformed with vectors encoding such nucleic acids such that the cellexpresses the inhibitory nucleic acid molecules. Transformation of thecells can be carried out according to any means suitable in the art.

A cell can be transfected with such nucleic acid molecules according toany means available in the art such as those describe or exemplifiedherein. It is preferred that cells are stably transfected with a vectorcomprising a nucleic acid sequence encoding such regulatory nucleic acidmolecules, although transiently transformations are suitable. Any vectorsuitable for transfection of the particular cell of interest can beused. In preferred embodiments, the vector is a viral vector. In someembodiments, the viral vector is a lentivirus vector.

The biologic activity of the vitamin D receptor, the vitamin D receptorsignal pathway constituent, or mutant p53 can be inhibited, for example,by contacting tumor cells with a compound, biomolecule, or compositionof a compound or a biomolecule that inhibits, inactivates, orantagonizes the biologic activity of the vitamin D receptor, the vitaminD receptor signal pathway constituent, or mutant p53 in the cell.Preferred biomolecules include peptide inhibitors and antibodies.

Non-limiting examples of compounds/agents that inhibit the biologicalactivity of the vitamin D receptor and/or its signal pathway includevitamin D receptor ligands, including vitamin D analogs and vitamin D3analogs that antagonize the vitamin D receptor in ways that enhancesensitivity of cells to PARP inhibitors. The ligand may be a vitamin Danalog. The vitamin D receptor ligand may be an antagonist of thevitamin D receptor. The ligand may comprise calcitriol, calcipotriol,eldecalcitol, lisinopril, elocalcitol, paricalcitol, seocalcitol, or anycombination thereof. The ligand may comprise TEI-9647, TEI-9648, or aderivative or analog thereof. Other suitable agents or analogs includethose described in Saito N et al. (2006) Chem. Biochem. 7:1478-90; DeebK K et al. (2007) Nature 7:684-700; Chiang K-C et al. (2009) World J.Gastroenterol. 15:3349-54, including 1-alpha,25-Dihydroxyvitamin D3 (aka1α,25(OH)₂D₃ or calcitriol), 2beta-(3-hydroxypropoxy)-1a,25(OH)₂D₃(ED-71 or eldecalcitol), lisinopril, elocalcitol, paricalcitol(19-nor-1alpha, 25(OH)₂D₂), seocalcitol (EB 1089), ILX23-7553,22-oxa-1,25-dihydroxyvitamin D3 (OCT), or any combination thereof.Calcitriol is preferred in some aspects. Paricalcitrol is preferred insome aspects. In some aspects, the VDR may be agonized instead ofantagonized, provided that agonism of the VDR inhibits homologousrecombination in the cell.

Without intending to be limited to any particular theory or mechanism ofaction, it is believed that tumor cells may express their own ligandthat binds to the VDR and directs DNA repair, for example, viahomologous recombination. Thus, to the extent a tumor cell expressessuch a ligand, the VDR ligand used in accordance with the invention maycompetitively inhibit this tumor cell ligand, in terms of VDR bindingand/or activation or potentiation.

The methods thus relate to a combination treatment, including the VDRligand and the PARP-1 inhibitor. It is preferred that the vitamin Dreceptor ligand negatively affects the homologous recombinationprocesses, e.g., inhibits it sufficiently for the PARP inhibitor to beefficacious in inducing tumor cell killing. For the combination, thecells may be contacted with the PARP inhibitor before the ligand,substantially contemporaneously with the ligand, or preferably, afterthe ligand. The combination of the VDR ligand and PARP inhibitorproduces a therapeutic synergy in killing tumor cells and in treatingtumors. The synergy is greater than the therapeutic effect of either theVDR ligand or the PARP inhibit or alone.

In some aspects, the methods further comprise inducing DNA damage, forexample, double stranded DNA breaks, in the DNA of the tumor cells. Thedamage may be induced in chromosomal DNA. Thus, the combination of DNAdamage such as double stranded breaks along with the inhibited/impairedhomologous recombination owing to the inactivation of the vitamin Dreceptor may make the cells more susceptible to PARP inhibition. DNAdamage may be induced according to any suitable means, including, forexample, by irradiating tumor cells, or by contacting the cells with aDNA damage-inducing agent. The DNA damage-inducing agent may be aplatinum-based chemotherapeutic agent. The DNA damage-inducing agent maycomprise gemcitabine. The combination of the VDR ligand, DNA damage suchas double stranded breaks, and PARP inhibitor produces a therapeuticsynergy in killing tumor cells and in treating tumors. The synergy isgreater than the therapeutic effect of the VDR ligand, DNA damage, orPARP inhibition alone.

The methods may be used to treat any cancer (or tumor type) in which thevitamin D receptor is expressed, or expressed at abnormal levels, or inwhich vitamin D receptor signaling mediates cancer development,progression, pathology, or resistance to one or more chemotherapeuticagents. Non-limiting examples of such cancers include pancreatic cancer,lung cancer (including non small cell lung cancer), bladder cancer,breast cancer, ovarian cancer esophageal cancer, prostate cancer, andlymphoma, among others, including any of these cancers in a metastaticstage. Pancreatic cancer is a highly preferred target of the methods.

The invention also features methods for treating a malignancy of thepancreas, lung, bladder, prostate gland, breast, ovary, lymph nodes, oresophagus comprising cells expressing the vitamin D receptor. In someaspects, the methods comprise transfecting a malignant cell of thepancreas, lung, bladder, prostate, breast, ovary, lymph nodes, oresophagus in the subject with a nucleic acid molecule that interfereswith the expression of the vitamin D receptor, and administering to thesubject an effective amount of a PARP-1 inhibitor. Transfection of thecells may be facilitated according to any technique suitable in the art.

In some aspects, the methods comprise administering to a subject in needthereof an effective amount of a nucleic acid molecule that interfereswith the expression of the vitamin D receptor and administering to thesubject an effective amount of a PARP-1 inhibitor. Followingadministration of the nucleic acid molecule, the nucleic acid moleculetransfects a malignant cell of the pancreas, lung, bladder, breast,ovary, prostate, lymph nodes, or esophagus expressing the vitamin Dreceptor and interferes with the expression of the gene encoding thevitamin D receptor. The nucleic acid molecule may be administered to orspecifically targeted to the cells of interest, or at least to an areaproximal to the cells of interest. Transfection of the cells may befacilitated according to any technique suitable in the art.

In some aspects, the methods comprise administering to a subject in needthereof an effective amount of a vitamin D receptor ligand and aneffective amount of a PARP inhibitor. The ligand may be a vitamin Danalog. The vitamin D receptor ligand may be an antagonist of thevitamin D receptor. The ligand may comprise calcitriol, calcipotriol,eldecalcitol, lisinopril, elocalcitol, paricalcitol, seocalcitol, or anycombination thereof. The ligand may comprise TEI-9647, TEI-9648, OU-72,or a derivative or analog thereof. The PARP-1 inhibitor may compriseolaparib, iniparib, rucaparib, veliparib, MK 4827, BMN673, BSI 401, orany combination thereof. The methods may further comprise inducing DNAdamage in tumor cells in the subject, for example, via irradiating thetumor cells or by administering to the subject an amount of gemcitabineeffective to induce DNA damage in the tumor cells. DNA damage preferablycomprises double stranded DNA breaks.

The agents (ligands, PARP inhibitors, gemcitabine, etc.) may beadministered according to any technique suitable in the art. The subjectto which the agents are administered may be any animal, preferablymammals, and including laboratory animals (e.g., rodents such as mice,rabbits, and rats), companion animals (e.g. cats and dogs), farm animals(e.g., horses, cows, pigs, sheep), and non-human primates. Human beingsare preferred subjects.

RAD51 is a protein related to DNA repair. RAD51 protein localizes tosites of DNA damage. It has been observed in accordance with theinvention that inhibition of the vitamin D receptor also blocksRAD51-mediated DNA damage repair. RAD51 may thus serve as a biomarkerfor vitamin D receptor inhibition. In particular, lack of RAD51localization to regions of DNA damage may signal the loss of vitamin Dreceptor expression or biologic activity. Lack of RAD51 localization toregions of DNA damage may signal inhibition of vitamin D receptorexpression or biologic activity.

The following examples are provided to describe the invention in greaterdetail. They are intended to illustrate, not to limit, the invention.

Example 1 Materials and Methods

Cell culture and chemicals. Panc1, BxPC3, and CFPAC1 cells werepurchased from American Type Culture Collection (ATCC) and banked inhouse until use. Cell lines were cultured in DMEM/10% FBS supplementedwith 2 mM glutamine and 1% penicillin, streptomycin, and kanamycin (PSK)and were maintained at 37° C. in 5% CO₂. Charcoal stripped (in housecell culture facility) and dialyzed FBS (Life Technologies; 50926400-036) were used. Gemcitabine was obtained from the in housepharmacy. Rucaparib and trichostatin A were gifts.

Plasmids. pLKO.1-VDRshRNA was purchased from Thermo Scientific(TRCN0000019504). pCMV-WT-VDR and pCMV-AMLVETO plasmids were made frombackbones obtained from Addgene. The VDR-S237M mutant was a gift. Tocreate the RNAi resistant allele, pCMV-WT-VDR was mutated at the VDRshRNA target sequence with conservative mutations at the wobble positionof 4 consecutive codons. VDR-C288G, K246G, and L254G mutants werecreated by Quick Change II mutagenesis (Agilent Technologies; 520200521).

Synthetic lethal RNAi Screen. High throughput RNAi was performed usingthe validated human genome-wide siRNA library version 2.0 obtained fromDharmacon. This is a SMARTPool (4 siRNAs per gene) library that targeted˜23,500 of the annotated genes, and has been validated to deplete mRNAby 75%. Stock siRNA was diluted in siRNA buffer (Dharmacon;B-002000-UB-100) and 10 ng of siRNA was reverse transfected into Panc1cells seeded into white Corning 384-well plates (Fisher Scientific;07-201-320) in quadruplicates on day 0. Briefly, diluted Dharmafectlreagent (Dharmacon; T-2001-01) in OptiMEM (Life Technologies; 51985091)was added to the wells and allowed to complex with siRNA for 20 minutesat room temperature. Panc1 cells in 100 μl of DMEM/10% FBS media withoutPSK were mixed with 100 μl of transfection mix at 1000 cells/well.Plates were incubated at 37° C. with 5% CO₂. After 48 hours, eithervehicle or gemcitabine (50 nM) was added and plates were furtherincubated for 48 hours. Total viable cell number was determined by theaddition of Cell Titer Glo (Promega; G7573) and relative luminescenceunits (RLU) were measured using an EnVision plate reader (Perkin Elmer).Raw RLU data was normalized to the mean siRNA control on each plate. Theeffect of gemcitabine treatment on viability was measured based on thenormalized viabilities in the drug treated and vehicle wells usingLimma. Statistical significance was measured by p-values controlled forthe false discovery rate (FDR) using the Benjamini-Hochberg step-upmethod to account for multiple testing. Hits showing an FDR of less than20% and also a change of at least 15% in viability relative to vehicletreated cells were selected for validation.

RNAseq data analysis. Raw sequence reads were aligned to the human hg19genome using the Tophat algorithm; Cufflinks algorithm was implementedto assemble transcripts and estimate their abundance. Cuffdiff was usedto statistically assess expression changes in quantified genes indifferent conditions.

Cell viability assays. For clonogenic assays, 1000 cells per well wereseeded into 6 well plates on day 0. Cells were treated with gemcitabineat various doses on day 1 for 24 hours. Gemcitabine was washed out onday 2, and cells were allowed to grow for a subsequent 10 days beforebeing fixed (10% methanol+10% acetic acid) and stained with crystalviolet (0.4% in 20% ethanol) for colony counting and quantitation. ForRucaparib clonogenic assays, the drug was added at various doses 24hours after cell plating, and cells were allowed to grow for asubsequent 10 days in the presence of Rucaparib. For TSA clonogenicassays, the drug was added for 4 hours prior to addition of gemcitabineor vehicle for another 18 hours before drugs were washed away, and cellswere allowed to grow in drug-free medium for 10 days.

Microscopy. For timelapse studies, Panc1 cells with stable expression ofHistone H2B fused at its C-terminus to GFP were seeded into 6-wellplates. 24 hours post cell plating, gemcitabine (50 nM) was added beforetimelapse was commenced. The plate was placed in a 37° C. chamber;bright-field and fluorescent images were taken every 5 minutes for 48hours using a Nikon TE2000S microscope controlled by Metamorph(Molecular Devices). Three independent movies were conducted for eachcondition. Movies were allowed to commence for 48 hours for eachindependent experiment.

For Immunofluorescence, cells were plated onto coverslips 24 hourspre-gemcitabine treatment. At different timepoints post gemcitabinetreatment, cells were permeablized, fixed (4% paraformaldehyde) andstained. Antibodies to γH2AX (Millipore; 05-636), Rad51 (a gift), and53BP1 were used. Alexa Fluor-conjugated (488, 555, and 647 nm) secondaryantibodies (Molecular probes; A-11029, A-21428, A-21247) were used at afinal concentration of 1 μg/ml and nuclei counterstained with DAPI.Images were captured using a 40× or 63× high NA objective mounted on asemi-automated inverted microscope (Nikon TEi) with a charge-coupleddevice camera (Photometrics1394) using Nikon Elements 2.0. Exposuretimes for antibodies were optimized for control samples and identicalexposure times used for the experimental samples. Images werequantitated and analyzed using Nikon Elements 2.0. Confocal images weretaken using a Leica TCS-SP8 microscope controlled by LAS software (LeicaMicrosystems).

Western Blotting. BxPC3, Panc1, and CFPAC1 cells were treated withvehicle or gemcitabine (50 nM) for 18 hrs. Cells were harvested, washedin PBS and lysed in NP40 lysis buffer (1% NP40/PBS/10% glycerol) withprotease and phosphatase inhibitors. Protein concentrations weredetermined with MicroBCA Assay (Pierce Biotechnology; 23224 and 23228)and then SDS sample buffer was added to the lysates. 40 μg of boiledlysates was separated by SDS-PAGE and then transferred onto Immobilon Pmembrane (Millipore; IPVH00010). Antibodies used for immunoblotting wereobtained from: VDR (Epitomics; 3277-1), γH2AX (Upstate Biotechnologies,now Millipore; 05-636), Rad51 (Genetex; GTX70230, gift), p300 (SantaCruz Biotchnologies; SC-584), and TAO1 kinase (Bethyl Labs; A300-524A).TAO1 was used as a loading control since its expression did not vary inany cell lines or drug treatments.

Example 2 RNAi Synthetic Lethality Screen to Enhance GemcitabineSensitivity

A genome-wide siRNA screen was performed to identify genes and pathwaysin Panc1 pancreatic adenocarinoma cells that can be targeted forgemcitabine sensitization. A sublethal dose (IC₂₀) of gemcitabine wasused (50 nM), which was sufficient to induce an S phase arrest and DNAdamage as seen by γH2AX foci. The low dose of gemcitabine (50 nM) mayalso be clinically relevant as it has been reported that only a smallpercentage of a chemotherapeutic dose of drugs actually reaches the PCatumor because of its dense stromal microenvironment.

Two days after siRNA transfection, gemcitabine or vehicle was added toduplicate plates and cell viability was assessed 48 hours later. Valueswere normalized to internal standards, as each plate contained negativeand positive controls, and comparisons made between vehicle andgemcitabine treated samples. Statistical analysis of the data was usedto rank the siRNAs according to their ability to enhance gemcitabinekilling. The false discovery rate (FDR) was determined for each sampleand a cutoff of 0.2 was used to identify 125 primary candidates.

Candidates were further validated for gemcitabine sensitization with aset of deconvolved siRNAs (4 individual siRNAs for each gene). 155 geneswere validated based on the ability of >2 of 4 deconvolved siRNAs toenhance gemcitabine killing. The validated hits were subjected topathway analysis using Ingenuity and STRING databases to assesspotential relationships with one another. A major gemcitabine survivalnetwork consisted of various DNA damage response genes involved inrepair and checkpoint functions (Chk1, Wee1, PIAS4, and 53BP1). Thisresult validated the screen and gave confidence to further evaluatecandidates not previously known to be involved in gemcitabine response.

Example 3 The Vitamin D Receptor (VDR) Sensitizes Pancreatic CancerCells to Gemcitabine

The Vitamin D Receptor (VDR) is a member of the superfamily of nuclearhormone receptors. Although the role of VDR in drug sensitization hasnot been documented, there have been reports that suggest a relationshipwith DNA damage. A positive feedback loop has been reported to existbetween the DNA damage checkpoint kinase, ATM, and VDR following DNAdamage. Notably, ATM and VDR expression were increased after DSBinduction by N-nitroso-N methylurea through ATM phosphorylation of VDRwhich in turn promoted VDR transactivation of the ATM gene. In addition,Vitamin D3 (1alpha,25(OH)₂D₃), which is the major ligand of the VDR, hasbeen shown to protect cells from genotoxic stress bypromoting DNArepair. Vitamin D3 (VD3) bound VDR is responsible for clearingcyclobutane pyrimidine dimers (CPDs) and pyrimidone photoproducts inmice that were exposed to UVB. Moreover, topically applied VD3 protectedskin from UV induced photodamage.

First, the sensitization achieved with VDR knockdown was compared tothat of Chk1 knockdown, a well-known chemosensitization target thatoverrides the DNA damage checkpoint and promotes mitotic catastrophe.Clonogenic assays were conducted, as this was more sensitive andreliable than the short term viability assays.

Panc1 cells transfected with control, VDR, and Chk1 siRNA's were treatedwith vehicle or 50 nM gemcitabine for 24 hours before drugs were washedout and cells seeded for clonogenic assays (FIG. 1, A). Colony formationdid not differ significantly in control siRNA samples treated withvehicle versus gemcitabine. Compared to control samples treated withgemcitabine, only 8% and 3% of the gemcitabine treated VDR and Chk1siRNAs transfected cells survived, respectively. Colony formation of 92%and 77% efficiency was seen for vehicle treated VDR and Chk1 siRNAstransfected cells, respectively.

These studies were extended to establish gemcitabine kill curvesfollowing control and VDR siRNA transfections of Panc1, BxPC3, andCFPAC1 cells. All three PCa cell lines showed increased sensitivity togemcitabine after knockdown of VDR (FIG. 1, B). BxPC3 cells treated withcontrol siRNA had a mean IC₅₀ of ˜200 nM as compared to the mean IC₅₀ of˜60 nM after transfection with VDR siRNA (p value of 0.036). CFPAC1cells treated with control siRNA had a mean IC₅₀ of ˜45 nM while theIC₅₀ of VDR depleted cells was reduced to ˜20 nM (p=0.083). Similarly,the IC₅₀ of control transfected Panc1 cells was reduced from ˜30 nM to˜18 nM after VDR knockdown.

To establish specificity of the VDR siRNA, a rescue of the sensitizationwas attempted by expressing RNAi resistant alleles of WT-VDR in cellsstably knocked down of VDR. A stable VDR knockdown cell line wasestablished by utilizing a lentiviral shRNA delivery system. BxPC3,Panc1, and CFPAC1 cells were infected with virus but only BXPC3 cellsthat were stably knocked down of VDR were recovered.

Western blots showed that BxPC3 VDRkd cells had ˜10 fold reduction ofVDR protein compared to the parental BxPC3 cells. Vector and WT-VDR weretransfected into the BxPC3 VDRkd cells and tested for gemcitabinesensitivity in clonogenic assays. As with the untransfected cells,vector transfected cells had an IC₅₀ of ˜50 nM gemcitabine. However,cells transfected with WT-VDR showed increased IC₅₀ of ˜300 nMgemcitabine (p=0.089) (FIG. 1, C).

To extend these results, various VDR mutants that are unable to activatetranscription were tested. Vitamin D3 is the major ligand that binds toVDR to activate transcription. In addition, transcription is usuallymediated by a heterodimer of VDR and RXR (retinoid acid X receptor).Mutations that disrupted ligand binding (C288G) and heterodimerization(K246G) (L254G) were transfected into the BxPC3 VDRkd cells but none ofthem rescued the gemcitabine sensitivity as with WT-VDR (FIG. 1, D). Asa further test for VDR specificity, two dominant negative mutants wereused to neutralize the ability of WT-VDR to restore gemcitabineresistance to the BXPC3 VDRkd cells. The S237M mutation in VDR preventsbinding by vitamin D3 but, unlike other ligand mutants, it exerts adominant negative effect by titrating away essential binding partnersfrom endogenous VDR.

Additionally, the AML1/ETO fusion oncogene that also sequesters VDR fromits binding partners, RXR and Runx2 was used, thus disrupting theformation of VDR transcriptional machinery. When WT-VDR wasco-transfected with either the S237M mutant or AML1/ETO into BxPC3 VDRkdcells, colony formation after gemcitabine treatment was reduced whencompared to just WT-VDR transfected cells (FIG. 1, D). The IC₅₀ forWT-VDR transfected cells was ˜260 nM while co-transfection of S237M orAML1/ETO reduced the IC₅₀s to ˜60 nM (p=0.039) and ˜80 nM (p=0.147)respectively, very similar to the IC₅₀ for the untransfected VDRknockdown cells. The combined data establish that both theligand-binding and heterodimerization domains are essential for VDR'srole in promoting gemcitabine survival.

Next, the levels of VDR protein were compared in BxPC3, CFPAC1, andPanc1 cells to see if the amount of expression might correlate withgemcitabine sensitivity. Western blots showed that the basal levels ofVDR differed amongst the cell lines such that BXPC3 had the highestamounts of VDR, followed by CFPAC1, and then Panc1 cells (FIG. 1, E).After overnight treatment with gemcitabine, VDR levels increased inPanc1 and CFPAC1 cells. No noticeable increase in VDR levels was seen inBXPC3. Comparison of the gemcitabine sensitivity showed that itnegatively correlated with VDR levels (FIG. 1, E) such that BxPC3 cellswith the highest levels of VDR had a mean IC₅₀ of ˜200 nM, while CFPAC1and Panc1 cells had IC₅₀'s of ˜45 nM and ˜30 nM, respectively.

Panc1 cells were used for VDR overexpression experiments to further testthe relationship between VDR and gemcitabine sensitivity. Cellstransfected with WT-VDR were significantly more resistant to gemcitabine(IC₅₀ ˜250 nM) than cells transfected with vector (IC₅₀ ˜25 nM) (FIG. 1,F). The VDR overexpression data supports the VDR knockdown data inestablishing that levels of VDR expression is a critical determinant forgemcitabine response in pancreatic cancer cells.

Example 4 VDR Specifies a Survival Pathway that is Distinct from the DNADamage Checkpoint Pathway

Since VDR knockdown achieved the same degree of gemcitabinesensitization as Chk1 knockdown, it was tested whether the mechanism ofVDR sensitization was due to checkpoint override. Time-lapse microscopywas used to track the fates of gemcitabine-treated Panc1 cells thatstably expressed a H2B:gfp fusion protein that labeled chromosomes.Cells were transfected with siRNAs, treated with vehicle or gemcitabineand monitored every 10 minutes for 48 hours (FIG. 2).

Control, VDR, or Chk1 siRNAs did not affect viability of vehicle treatedcells as their numbers increased at the end of 48 hours. Addition ofgemcitabine to control siRNA cells stopped proliferation as a result ofthe checkpoint, but cells did not die during the span of the timelapseexperiment.

Chk1 knockdown abrogated the cell cycle arrest mediated by gemcitabineas cells were observed to enter mitosis where many died or died shortlyafter exit from mitosis. By contrast, cells transfected with VDR siRNAnever entered mitosis, but nevertheless died during the span of the ˜48hour timelapse. It is believed that Gemcitabine sensitization after VDRknockdown is not due to override of the DNA damage checkpoint pathwaymediated by Chk1.

Example 5 VDR Knockdown Impairs Foci Formation by DNA Damage ResponseProteins Gamma-H2AX, 53BP1, and Rad51 Following Gemcitabine Treatment

It was next investigated if drug sensitization after VDR knockdown mightbe due to defective DNA damage repair. Gemcitabine is a nucleosideanalog that acts as a chain terminator that will stall replicationforks. If the forks cannot restart, they collapse to form DNA doublestrand breaks that can be detected by the formation of phospho-γH2AXfoci. Repair of stalled forks is mediated by the error-free homologousrecombination pathway (HR). Rad51, an essential component of HR, hasbeen implicated in promoting gemcitabine resistance in non-small-celllung cancer and pancreatic cancer. 53BP1, on the other hand, protectsdouble stranded break ends from resection, which is required for HR, topromote non-homologous end-joining (NHEJ) which is an error-prone repairpathway.

It was investigated if these repair pathways were abrogated after VDRknockdown by staining for foci formation by phospho-γH2AX, Rad51, and53BP1, and measuring intensities after gemcitabine treatment (FIGS. 3,4, and 5). BxPC3 (high VDR expression) and Panc1 (low VDR expression)cells were treated with gemcitabine (50 nM) for 2, 4, 8, and 18 hours,and fixed and stained for phospho-γH2AX, 53BP1, and Rad51. Fociquantitation included counting of nuclei with >5 foci and a separatemeasurement of the sum intensities of foci that were averaged for 5separate immunofluorescence experiments. Thus, the foci counts do notreflect their intensities, which were quantitated separately. Weak butdetectable phospho-γH2AX foci were visible within 4 hours of gemcitabinetreatment in BxPC3 cells while it took 18 hours for foci to form inPanc1 cells (FIG. 3, A). Similarly, Rad51 foci were visible after 8hours of gemcitabine treatment in BxPC3 cells compared to 18 hours inPanc1 cells (FIG. 3, A, FIG. 4, and FIG. 5). The kinetics of 53BP1 fociformation were comparable between the two cell lines.

Next, it was investigated whether VDR deficiency affected the kineticsof foci formation in BxPC3 and Panc1 cells. The kinetics of fociformation in the BxPC3 VDRkd cells were compared to the foci formationobserved in the parental cells. Transient siRNA transfections were usedto knockdown VDR in the Panc1 cells. VDR knockdown delayed fociformation and reduced foci intensities of phospho-γH2AX and Rad51 inboth cell lines (FIG. 3, A, FIG. 4, and FIG. 5). 53BP1 foci formationkinetics did not seem to be affected by VDR knockdown in either cellline (FIG. 3, A, FIG. 4, and FIG. 5). Phospho-γH2AX and Rad51 foci inBxPC3 VDRkd cells were detected 8 and 18 hours, respectively, followingaddition of gemcitabine as compared to 4 and 8 hours, respectively, inthe parental cells. Similarly, Panc1 cells transfected with VDR siRNAdid not exhibit phospho-γH2AX and Rad51 foci until 18 hours followinggemcitabine addition as compared to ˜8 hours for Panc1 cells transfectedwith control. The slower kinetics of foci formation in Panc1 cells wasaccelerated by transient VDR overexpression in Panc1 cells (FIG. 5).

Along with the delayed kinetics foci formation and reduced intensitiesof phospho-γH2AX and Rad51 after VDR knockdown, qualitative differenceswere observed in the staining patterns of Rad51, 53BP1, andphospho-γH2AX. Parental BxPC3 cells form discrete punctate phospho-γH2AXfoci compared to the VDRkd cells that displayed a diffuse, pan nuclearphospho-γH2AX staining pattern (FIG. 3, B). The punctate pattern isindicative of damage recognition and subsequent repair complex formationnear the sites of damage. In contrast, the diffuse pattern is indicativeof damage recognition, but is believed to reflect a failure to retainrepair complexes distal to damage sites which leads to furtheraccumulation of DNA damage that eventually leads to catastrophic celldeath.

Phospho-γH2AX formed punctate foci 18 hours after gemcitabine treatmentin 94% of the parental BxPC3 cells. By contrast, punctate foci were seenin only 18% of the VDRkd cells and the remaining 82% of the cellsexhibited a diffuse pattern (FIG. 3, B). Although the kinetics of fociformation by 53BP1 was not affected by VDR knockdown (FIG. 3, A), italso exhibited a more diffuse 53BP1 staining pattern as seen forphospho-γH2AX (FIG. 3B). After 18 hours of gemcitabine treatment, 90% ofthe parental cells formed punctate 53BP1 foci and 10% expressed thediffuse pattern. This contrasts with only 31% of the VDRkd cells formedpunctate foci while 69% expressed the diffuse pattern.

Similarly, Rad51 foci formation was also compromised in the VDRkd cells.After 18 hours of gemcitabine treatment, 92% of the parental BxPC3 cellsexhibited clear Rad51 foci as compared to 28% of the VDRkd cells. 72% ofVDRkd cells (which were also phospho-γH2AX positive) exhibited diffuseRad51 staining as compared to only 8% that were seen in the parentalcells (FIG. 3, B). Therefore, VDR knockdown not only delays the kineticsof foci formation of phospho-γH2AX and Rad51, but also compromises theability of phospho-γH2AX, 53BP1, and Rad51 to form punctate foci.

The reduction in Rad51 foci formation in gemcitabine treated cellsdepleted of VDR suggested an impairment in HR. To functionally testwhether HR has been compromised after VDR knockdown, the sensitivity ofparental and VDR knockdown cells to the PARP inhibitor Rucaparib wascompared. This is based on the observation that PARP inhibitorsselectively kill BRCA1 defective cells because of their HR deficiency.Furthermore, PARP inhibition has been shown to increase Rad51 foci, anddepletion of Rad51 sensitized cells to PARP inhibition.

BxPC3 and Panc1 cells were transfected with control, VDR, and BRCA1siRNAs and their sensitivity to Rucaparib treatment was compared byclonogenic survival. The results clearly showed that VDR knockdownrendered both cell lines more sensitive to Rucaparib than the controls.For BXPC3 cells, the IC₅₀s after knockdown of BRCA1 and VDR were 1 and 5uM, respectively (FIG. 6, A) compared to the control IC50 of 9 μM. ForPanc1 cells, the IC₅₀s after knockdown of BRCA1 and VDR were 3.5 and 400nM, respectively (FIG. 4, A) compared to the control (IC₅₀=4 μM). Thedifference in sensitivities to Rucaparib between VDR and BRCA1 knockdownwas due to the fact that Rad51 foci formation was more efficientlyinhibited in BRCA1 depleted cells. The increased sensitivity of cellsdepleted of VDR to Rucaparib supports the data that suggests Rad51mediated HR functions are impaired.

As VDR is a transcription factor, it may regulate the expression of DNArepair genes such as Rad51 and γH2AX. Comparison of the levels of thesetwo proteins between parental and after VDR knockdown did not show asignificant difference that would account for the reduced ability toform DNA damage foci induced by gemcitabine. Western blots wereperformed to assay VDR's role in regulating the expression of γH2AX,53BP1, and Rad51 after DNA damage induction. Parental and BxPC3 VDRkdcells treated with gemcitabine for 18 hours expressed equivalent amountsof Rad51 and H2AX in whole cell extracts (supernatants) (FIG. 6, B).However, analysis of the chromatin fractions showed very low amounts ofRad51 and phospho-γH2AX in VDRkd cells compared to the parental BxPC3cells (FIG. 6, B). This supported the staining data that Rad51 andphospho-γH2AX foci formation were impaired in VDR depleted cells treatedwith gemcitabine. To further examine if VDR might be regulating theexpression of these and other DNA damage response genes, RNAseq was usedto compare the transcriptomes of BXPC3 parental and VDRkd cells of Rad51and H2AX. This analysis did not identify significant differences intheir mRNA levels though the transcript numbers were slightly (<2 fold)reduced in the BxPC3 VDRkd cells compared to the parental BxPC3 cells.

Rad51 foci formation has been shown to depend on histone acetylation.The histone acetyltransferases TIP48, 49, and 60 have been shown tomodulate Rad51 foci formation in response to DNA damage through histoneacetylation. Given that VDR forms complexes with coactivators thatcontain histone acetylases and corepressors that contain HDACs, it mayuse this activity to specify Rad51 foci formation. VDRkd cells weretreated with the HDAC inhibitor, Trichostain A (TSA) (500 nM), and Rad51foci formation after gemcitabine treatment (50 nM) were monitored (FIG.6, C). In the absence of TSA, 11% of the VDRkd cells exhibited Rad51foci after 4 hrs in gemcitabine as compared to 89% positive cells afterTSA treatment. This increase was comparable to parental cells where 92%of the cells exhibited Rad51 foci within 4 hours of gemcitabinetreatment.

To test the functional relevance of the TSA mediated Rad51 fociformation in the VDR knockdown cells, whether TSA altered thesensitivity to gemcitabine was investigated. Using the sameconcentration of TSA (500 nM) that restored the kinetics of Rad51 fociformation, it did not render the VDRkd cells more sensitive togemcitabine than cells without TSA treatment (both treatments had anIC₅₀ of 50 nM of gemcitabine) (FIG. 6, D). Parental cell sensitivity togemcitabine was increased by TSA treatments at the concentrations tested(p=0.02). The IC₅₀ for the gemcitabine plus TSA treated cells was 100 nMcompared to cells treated with gemcitabine alone which had an IC₅₀ of˜200 nM (FIG. 6, D).

The contribution of the p300 HAT (histone acetyltransferase) in Rad51foci formation was tested because p300 interacts with VDR to activatetranscription of specific target genes. p300 also has been shown todirectly promote Rad51 transcription following DSB induction in lungcancer cell lines. First, p300 was depleted from BxPC3 and Panc1 cellsusing shRNAs, and cells were treated with gemcitabine and Rad51 fociformation were monitored over time. The number of Rad51 foci and overallintensity was reduced in the p300 shRNA transfected cells compared tocontrol cells (FIG. 7A,). Of the BxPC3 cells transfected with p300shRNA, ˜22% were positive for Rad51 foci (>5 foci/nucleus) compared to˜84% of the control cells 18 hrs post gemcitabine treatment. Overall,Rad51 focal intensity was also reduced by ˜35% in the p300 knockdowncells compared to control cells. Gemcitabine sensitivity was also testedafter p300 knockdown (FIG. 7, B). Consistent with the decreased Rad51foci, p300 knockdown effectively sensitized BxPC3 cells to gemcitabine.The control shRNA treated cells had an IC₅₀ of ˜80 nM while the p300shRNA treated cells had an IC₅₀ of ˜40 nM (p=0.0489). Panc1 cells alsodid not exhibit increased sensitivity to gemcitabine following p300knockdown with the IC₅₀s of p300 knockdown cells and control cells beingsimilar at ˜16 nM and ˜19 nM, respectively.

Example 6 Summary

Twenty seven target genes that contributed to gemcitabine survival inPanc1 cells were identified. Analysis by STRING and Ingenuity identifiedtwo networks that specified gemcitabine survival. One was the DNA damageresponse network that consisted of CHK1, Wee1, PIAS4, and 53BP1. Thesegenes validated the screen. VDR was part of a second network that alsoincluded SRF, and MMP13. Runx2, a VDR binding partner and transcriptionfactor, activates the MMP13 gene during prostate cancer invasion andmetastasis. Similarly, RXR-alpha, a major VDR binding partner, directlyinteracts with SRF and has been shown to compete with SRF for otherbinding partners like SRC-1 and p300. An acetylcholinestarase (ACHE), adehydrogenase (BCKDHB), phosphatases (DUSP23 and EPM2A), a transferase(GSTM3), a member of the pyruvate dehydrogenase complex (PDHA1),serine/threonine kinase (STK39), a cysteine peptidase (APG4D), atransporter (TNP02), and transcriptional regulators (TBX4, TBX5, andKLF10) were identified.

It is believed that the VDR is a novel target for gemcitabinesensitization, and its knockdown enhanced gemcitabine killing aseffectively as with Chk1 knockdown. However, the mechanism ofsensitization is not via checkpoint override but rather to a previouslyunknown role of VDR in Rad51 mediated DNA repair. The data showed thatVDR is required for the recruitment of Rad51, a key protein inerror-free homologous recombination (HR) and is a determinant ofgemcitabine sensitivity because of its role in repairing stalledreplication forks.

The levels of VDR varied amongst Panc1, BXPC3 and CFPAC cells, and cellswith higher levels were more resistant to gemcitabine. For all the celllines, knockdown of VDR increased their sensitivity to gemcitabine.BXPC3 cells, which were most resistant to gemcitabine (IC₅₀ ˜200 nM),showed the greatest reduction (˜3-fold) in IC₅₀ after depletion of VDR.Transfection of wild type VDR into the VDR depleted BXPC3 cellsincreased the IC₅₀ ˜6-fold over vector controls, and to levels seen forthe parental BXPC3 cells. Consistent with this observation, increasingVDR levels in Panc1 cells (which has less VDR than BXPC3 cells)increased their IC₅₀ to gemcitabine by ˜10-fold over controls.

The effects of VDR on gemcitabine sensitivity is ligand and dimerizationdependent as VDR mutants lacking these activities failed to rescue thegemcitabine sensitivity of cells depleted of VDR. Furthermore, dominantnegative mutants such as VDR S237M and the AML1/ETO oncogene fusion,both of which have been shown to sequester VDR from its partners such asRXR and Runx2, failed to rescue gemcitabine sensitivity. Despite theligand dependence for gemcitabine survival, it is unclear if VD3 (1,25dihydroxyvitamin D) is the ligand.

These studies were conducted using charcoal stripped and dialyzed serumthat does not support VDR dependent transcription in the absence of anexogenous source of ligand. It is known that VDR can bind other ligandssuch as curcumin and lithocholic acid, the latter of which is a toxicbile acid that activates VDR-dependent transcription of the CYP3Adetoxifying gene that is independent of VD3.

It was showed that VDR was essential for pancreatic cancer cells to formRad51 and foci in response to gemcitabine. In BxPC3 cells that expressedthe highest levels of VDR, Rad51 and phospho-γH2AX foci form 8 and 4hours respectively, after addition of gemcitabine and the number andintensity of foci increase for up to 18 hours. In Panc1 cells which havelower VDR levels, or when VDR was experimentally depleted from BXPC3cells, the kinetics of Rad51 and phospho-γH2AX foci formation wasdelayed by 4 and 6 hours respectively, and the intensity of the foci wasreduced 1.5 and 2 fold respectively, and never reached the levels seenin control cells. Furthermore, the diffuse staining pattern of Rad51 andphospho-γH2AX that is seen in the nuclei of VDR depleted cells has beeninterpreted to reflect catastrophic amounts of DNA damage.

Without intending to be limited to any particular theory or mechanism ofaction, it is believed that VDR facilitates Rad51 dependent homologousrecombination. Both BxPC3 and Panc1 cells were sensitized to the PARPinhibitor Rucaparib after VDR knockdown when compared to control cells.It was also observed that the levels of VDR negatively correlated withRucaparib sensitivity as Panc1 cells (which has less VDR) were moresensitive to Rucaparib than BxPC3 cells. These data suggest that thelevel of VDR expression may be a determinant of HR repair efficiency inPCa cells and, thus, may be used as a predictive marker for PARPinhibitors.

The mechanism by which VDR facilitates Rad51 foci formation does notappear to be at the level of transcription. Cells depleted of VDRexpressed Rad51 protein at levels comparable to control cells. This wascorroborated by RNAseq data which showed no significant difference inmRNA levels of not only Rad51 but many of the proteins that are known tobe important for Rad51 foci formation. The defect lies at the level ofrecruitment of Rad51 to sites of damage.

The defect may be at the level of histone acetylation which is known tobe important for Rad51 formation. Indeed, Rad51 foci formation in VDRdepleted cells can be rescued with an HDAC inhibitor (TSA). However, TSAdid not increase gemcitabine resistance as it may exert other effectsthat are toxic to cells. Conversely, when the p300 HAT was depleted fromVDR expressing cells, they failed to form Rad51 foci after gemcitabinetreatment.

The invention is not limited to the embodiments described andexemplified above, but is capable of variation and modification withinthe scope of the appended claims.

We claim:
 1. A method for killing tumor cells expressing the vitamin Dreceptor, comprising contacting the tumor cells with a vitamin Dreceptor ligand in an amount effective to inhibit homologousrecombination in the tumor cells, and contacting the tumor cells with atherapeutically effective amount of a Poly(ADP) Ribose Polymerase 1(PARP-1) inhibitor, wherein the combination of the vitamin D receptorligand and the PARP-1 inhibitor exhibits therapeutic synergy in killingthe tumor cells.
 2. The method of claim 1, wherein the tumor cells arepancreatic tumor cells, lung tumor cells, breast tumor cells, ovariantumor cells, lymph node tumor cells, bladder tumor cells, prostate tumorcells, or esophageal tumor cells.
 3. The method of claim 1, wherein thetumor is a tumor cells are pancreatic tumor cells.
 4. The method ofclaim 1, wherein the vitamin D receptor ligand is a vitamin D receptorantagonist.
 5. The method of claim 4, wherein the vitamin D receptorantagonist is a vitamin D analog.
 6. The method of claim 1, wherein thevitamin D receptor ligand is selected from the group consisting ofcalcitriol, calcipotriol, eldecalcitol, lisinopril, elocalcitol,paricalcitol, seocalcitol, TEI-9647, TEI-9648, OU-72, and a combinationthereof.
 7. The method of claim 1, further comprising inducing doublestranded DNA breaks in the chromosomal DNA of the tumor cells.
 8. Themethod of claim 7, wherein inducing double stranded DNA breaks comprisesirradiating the chromosomal DNA of the tumor cells.
 9. The method ofclaim 7, wherein inducing double stranded DNA breaks comprisescontacting the tumor cells with an amount of gemcitabine effective toinduce double stranded DNA breaks.
 10. The method of claim 1, whereinthe tumor cells expressing the vitamin D receptor are resistant to thePARP-1 inhibitor.
 11. The method of claim 1, wherein the PARP-1inhibitor is selected from the group consisting of olaparib, iniparib,rucaparib, veliparib, MK 4827, BMN673, BSI 401, and a combinationthereof.
 12. The method of claim 10, wherein the PARP-1 inhibitor isselected from the group consisting of olaparib, iniparib, rucaparib,veliparib, MK 4827, BMN673, BSI 401, and a combination thereof.
 13. Themethod of claim 3, wherein the method comprises contacting thepancreatic tumor cells with a vitamin D receptor ligand in an amounteffective to inhibit homologous recombination in the pancreatic tumorcells, and then contacting the pancreatic tumor cells with atherapeutically effective amount of the PARP-1 inhibitor, wherein thecombination of the vitamin D receptor ligand and the PARP-1 inhibitorexhibits therapeutic synergy in killing the pancreatic tumor cells. 14.The method of claim 13, wherein the PARP-1 inhibitor is selected fromthe group consisting of olaparib, iniparib, rucaparib, veliparib, MK4827, BMN673, BSI 401, and a combination thereof.
 15. The method ofclaim 14, wherein the pancreatic tumor cells are resistant to the PARP-1inhibitor.
 16. The method of claim 13, further comprising inducingdouble stranded DNA breaks in the chromosomal DNA of the pancreatictumor cells.
 17. The method of claim 16, wherein inducing doublestranded DNA breaks comprises irradiating the chromosomal DNA of thepancreatic tumor cells.
 18. The method of claim 16, wherein inducingdouble stranded DNA breaks comprises contacting the pancreatic tumorcells with an amount of gemcitabine effective to induce double strandedDNA breaks in the chromosomal DNA.
 19. The method of claim 14, whereinthe vitamin D receptor ligand is a vitamin D analog.
 20. The method ofclaim 14, wherein the vitamin D receptor ligand is selected from thegroup consisting of calcitriol, calcipotriol, eldecalcitol, lisinopril,elocalcitol, paricalcitol, seocalcitol, TEI-9647, TEI-9648, OU-72, and acombination thereof.